I am currently trying to run the RealignerTargetCreator on some bam files which were aligned to hg19 howver am getting this error
`ERROR MESSAGE: Input files known and reference have incompatible contigs: Found contigs with the same name but different lengths:

ERROR contig known = chrM / 16571

ERROR contig reference = chrM / 16569.`

After some initial investigation I found that the supplied hg19 reference genome which was being used for mapping was using rCRS mtDNA. other then realigning to a different build of hg19 is there any way to easily fix this problem through GATK?